Human and mouse proteases: a comparative genomic approach (original) (raw)

• Barrett, A. J., Rawlings, N. D. & Woessner, J. F. Handbook of Proteolytic Enzymes (Academic Press, San Diego, 1998). An essential book in the protease field that comprehensively lists and describes proteases from many organisms.
  Google Scholar
• Hooper, N. M. Proteases in Biology and Medicine (Portland Press, London, 2002).
  Google Scholar
• Egeblad, M. & Werb, Z. New functions for the matrix metalloproteinases in cancer progression. Nature Rev. Cancer 2, 161–174 (2002). This review illustrates the diversity of protease functions in pathological processes such as cancer.
  CAS Google Scholar
• Krane, S. M. Elucidation of the potential roles of matrix metalloproteinases in skeletal biology. Arthritis Res. Ther. 5, 2–4 (2003).
  CAS PubMed Google Scholar
• Esler, W. P. & Wolfe, M. S. A portrait of Alzheimer secretases — new features and familiar faces. Science 293, 1449–1454 (2001).
  CAS PubMed Google Scholar
• Luttun, A., Dewerchin, M., Collen, D. & Carmeliet, P. The role of proteinases in angiogenesis, heart development, restenosis, atherosclerosis, myocardial ischemia, and stroke: insights from genetic studies. Curr. Atheroscler. Rep. 2, 407–416 (2000).
  CAS PubMed Google Scholar
• Uría, J. A. & López-Otín, C. Matrilysin-2, a new matrix metalloproteinase expressed in human tumors and showing the minimal domain organization required for secretion, latency, and activity. Cancer Res. 60, 4745–4751 (2000).
  PubMed Google Scholar
• Geier, E. et al. A giant protease with potential to substitute for some functions of the proteasome. Science 283, 978–981 (1999).
  CAS PubMed Google Scholar
• Voges, D., Zwickl, P. & Baumeister, W. The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu. Rev. Biochem. 68, 1015–1068 (1999).
  CAS PubMed Google Scholar
• López-Otín, C. & Overall, C. M. Protease degradomics: a new challenge for proteomics. Nature Rev. Mol. Cell Biol. 3, 509–519 (2002). This article introduces new concepts and approaches for the global analysis of proteases in normal and pathological conditions, and especially in cancer.
  Google Scholar
• Rawlings, N. D., O'Brien, E. & Barrett, A. J. MEROPS: the protease database. Nucleic Acids Res. 30, 343–346 (2002). A description of a database that is freely available to the academic community, which represents an essential resource for research on proteases.
  CAS PubMed PubMed Central Google Scholar
• International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
• Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).
  CAS PubMed Google Scholar
• Zucker, S. & Chen, W. -T. Cell Surface Proteases (Academic Press, San Diego, 2003). A compilation of articles that cover recent advances in the functional analysis of membrane-bound proteases, which are a group of enzymes that are of growing relevance in normal and pathological conditions.
  Google Scholar
• Cope, G. A. et al. Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science 298, 608–611 (2002).
  CAS PubMed Google Scholar
• Urban, S., Lee, J. R. & Freeman, M. A family of Rhomboid intramembrane proteases activates all Drosophila membrane-tethered EGF ligands. EMBO J. 21, 4277–4286 (2002).
  CAS PubMed PubMed Central Google Scholar
• Mariño, G. et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy. J. Biol. Chem. 278, 3671–3678 (2003).
  PubMed Google Scholar
• Weihofen, A., Binns, K., Lemberg, M. K., Ashman, K. & Martoglio, B. Identification of signal peptide peptidase, a presenilin-type aspartic protease. Science 296, 2215–2218 (2002).
  CAS PubMed Google Scholar
• Makarova, K. S., Aravind, L. & Koonin, E. V. A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. Trends Biochem. Sci. 25, 50–52 (2000).
  CAS PubMed Google Scholar
• Krylov, D. M. & Koonin, E. V. A novel family of predicted retroviral-like aspartyl proteases with a possible key role in eukaryotic cell cycle control. Curr. Biol. 11, 584–587 (2001).
  Google Scholar
• Mouse Genome Sequence Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).
• Swanson, W. J. & Vacquier, V. D. The rapid evolution of reproductive proteins. Nature Rev. Genet. 3, 137–144 (2002).
  CAS PubMed Google Scholar
• Balbín, M. et al. Identification and enzymatic characterization of two diverging murine counterparts of human interstitial collagenase (MMP-1) expressed at sites of embryo implantation. J. Biol. Chem. 276, 10253–10262 (2001).
  PubMed Google Scholar
• Deussing, J. et al. Identification and characterization of a dense cluster of placenta-specific cysteine peptidase genes and related genes on mouse chromosome 13. Genomics 79, 225–240 (2002).
  CAS PubMed Google Scholar
• Sol-Church, K. et al. Evolution of placentally expressed cathepsins. Biochem. Biophys. Res. Commun. 293, 23–29 (2002).
  CAS PubMed Google Scholar
• Yeh, E. T., Gong, L. & Kamitani, T. Ubiquitin-like proteins: new wines in new bottles. Gene 248, 1–14 (2000).
  CAS PubMed Google Scholar
• Brachvogel, B. et al. Molecular cloning and expression analysis of a novel member of the disintegrin and metalloprotease-domain (ADAM) family. Gene 288, 203–210 (2002).
  CAS PubMed Google Scholar
• Olsson, A. Y. & Lundwall, A. Organization and evolution of the glandular kallikrein locus in Mus musculus. Biochem. Biophys. Res. Commun. 299, 305–311 (2002).
  PubMed Google Scholar
• Yousef, G. M. & Diamandis, E. P. The new human tissue kallikrein gene family: structure, function, and association to disease. Endocr. Rev. 22, 184–204 (2001).
  CAS PubMed Google Scholar
• Luo, L. Y. et al. The serum concentration of human kallikrein 10 represents a novel biomarker for ovarian cancer diagnosis and prognosis. Cancer Res. 63, 807–811 (2003).
  CAS PubMed Google Scholar
• Balk, S. P., Ko, Y. J. & Bubley, G. J. Biology of prostate-specific antigen. J. Clin. Oncol. 21, 383–391 (2003).
  CAS PubMed Google Scholar
• Caputo, E., Manco, G., Mandrich, L. & Guardiola, J. A novel aspartyl proteinase from apocrine epithelia and breast tumors. J. Biol. Chem. 275, 7935–7941 (2000).
  CAS PubMed Google Scholar
• Yoshida, M., Kaneko, M., Kurachi, H. & Osawa, M. Identification of two rodent genes encoding homologues to seminal vesicle autoantigen: a gene family including the gene for prolactin-inducible protein. Biochem. Biophys. Res. Commun. 281, 94–100 (2001).
  CAS PubMed Google Scholar
• Lunderius, C. & Hellman, L. Characterization of the gene encoding mouse mast cell protease 8 (mMCP-8), and a comparative analysis of hematopoietic serine protease genes. Immunogenetics 53, 225–232 (2001).
  CAS PubMed Google Scholar
• Garnier, G., Circolo, A., Xu, Y. & Volanakis, J. E. Complement C1r and C1s genes are duplicated in the mouse: differential expression generates alternative isomorphs in the liver and in the male reproductive system. Biochem. J. 371, 631–640 (2003).
  CAS PubMed PubMed Central Google Scholar
• Nishimura, H. et al. The ADAM1a and ADAM1b genes, instead of the ADAM1 (fertilin-α) gene, are localized on mouse chromosome 5. Gene 291, 67–76 (2002).
  CAS PubMed Google Scholar
• Grima, J., Wong, C. C., Zhu, L. J., Zong, S. D. & Cheng, C. Y. Testin secreted by Sertoli cells is associated with the cell surface, and its expression correlates with the disruption of Sertoli-germ cell junctions but not the inter-Sertoli tight junction. J. Biol. Chem. 273, 21040–21053 (1998).
  CAS PubMed Google Scholar
• Fischer, H., Koenig, U., Eckhart, L. & Tschachler, E. Human caspase 12 has acquired deleterious mutations. Biochem. Biophys. Res. Commun. 293, 722–726 (2002).
  CAS PubMed Google Scholar
• Grzmil, P. et al. Human cyritestin genes (CYRN1 and CYRN2) are non-functional. Biochem. J. 357, 551–556 (2001).
  CAS PubMed PubMed Central Google Scholar
• O'Sullivan, C. M., Liu, S. Y., Karpinka, J. B. & Rancourt, D. E. Embryonic hatching enzyme strypsin/ISP1 is expressed with ISP2 in endometrial glands during implantation. Mol. Reprod. Dev. 62, 328–334 (2002).
  CAS PubMed Google Scholar
• Kageyama, T. Pepsinogens, progastricsins, and prochymosins: structure, function, evolution, and development. Cell. Mol. Life Sci. 59, 288–306 (2002).
  CAS PubMed Google Scholar
• Rose, S. D. & MacDonald, R. J. Evolutionary silencing of the human elastase I gene (ELA1). Hum. Mol. Genet. 6, 897–903 (1997).
  CAS PubMed Google Scholar
• Suzuki, H. & Kumagai, H. Autocatalytic processing of γ-glutamyltranspeptidase. J. Biol. Chem. 277, 43536–43543 (2002).
  CAS PubMed Google Scholar
• Paulding, C. A., Ruvolo, M. & Haber, D. A. The Tre2 (USP6) oncogene is a hominoid-specific gene. Proc. Natl Acad. Sci. USA 100, 2507–2511 (2003).
  CAS PubMed PubMed Central Google Scholar
• Fougerousse, F. et al. Human–mouse differences in the embryonic expression patterns of developmental control genes and disease genes. Hum. Mol. Genet. 9, 165–173 (2000).
  CAS PubMed Google Scholar
• Emes, R. D., Goodstadt, L., Winter, E. E. & Ponting, C. P. Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum. Mol. Genet. 12, 701–709 (2003). An excellent analysis of the differences among human and mouse genomes and discussion of their physiological relevance.
  CAS PubMed Google Scholar
• Salamonsen, L. A. & Nie, G. Proteases at the endometrial–trophoblast interface: their role in implantation. Rev. Endocr. Metab. Disord. 3, 133–143 (2002).
  CAS PubMed Google Scholar
• Fata, J. E., Ho, A. T., Leco, K. J., Moorehead, R. A. & Khokha, R. Cellular turnover and extracellular matrix remodeling in female reproductive tissues: functions of metalloproteinases and their inhibitors. Cell. Mol. Life Sci. 57, 77–95 (2000).
  CAS PubMed Google Scholar
• Curry, T. E. & Osteen, K. G. Cyclic changes in the matrix metalloproteinase system in the ovary and uterus. Biol. Reprod. 64, 1285–1296 (2001).
  CAS PubMed Google Scholar
• Evans, J. P. Fertilin-β and other ADAMs as integrin ligands: insights into cell adhesion and fertilization. Bioessays 23, 628–639 (2001).
  CAS PubMed Google Scholar
• Seals, D. F. & Courtneidge, S. A. The ADAMs family of metalloproteases: multidomain proteins with multiple functions. Genes Dev. 17, 7–30 (2003).
  CAS PubMed Google Scholar
• Ny, T., Wahlberg, P. & Brandstrom, I. J. Matrix remodeling in the ovary: regulation and functional role of the plasminogen activator and matrix metalloproteinase systems. Mol. Cell Endocrinol. 187, 29–38 (2002).
  CAS PubMed Google Scholar
• Hulboy, D. L., Rudolph, L. A. & Matrisian, L. M. Matrix metalloproteinases as mediators of reproductive function. Mol. Hum. Reprod. 3, 27–45 (1997).
  CAS PubMed Google Scholar
• Vu, T. H. & Werb, Z. Matrix metalloproteinases: effectors of development and normal physiology. Genes Dev. 14, 2123–2133 (2000).
  CAS PubMed Google Scholar
• Overall, C. M. Molecular determinants of metalloproteinase substrate specificity: matrix metalloproteinase substrate binding domains, modules, and exosites. Mol. Biotechnol. 22, 51–86 (2002).
  CAS PubMed Google Scholar
• Mahon, P. & Bateman, A. The PA domain: a protease-associated domain. Protein Sci. 9, 1930–1934 (2000).
  CAS PubMed PubMed Central Google Scholar
• Luo, X. & Hofmann, K. The protease-associated domain: a homology domain associated with multiple classes of proteases. Trends Biochem. Sci. 26, 147–148 (2001).
  CAS PubMed Google Scholar
• Llamazares, M., Cal, S., Quesada, V. & López-Otín, C. Identification and characterization of ADAMTS-20 defines a novel subfamily of metalloproteinases-disintegrins with multiple thrombospondin-1 repeats and a unique GON-domain. J. Biol. Chem. 278, 13382–13389 (2003).
  CAS PubMed Google Scholar
• Somerville, R. P. et al. Characterization of ADAMTS-9 and ADAMTS-20 as a distinct ADAMTS subfamily related to Caenorhabditis elegans GON-1. J. Biol. Chem. 278, 9503–9513 (2003).
  CAS PubMed Google Scholar
• Hooper, J. D., Clements, J. A., Quigley, J. P. & Antalis, T. M. Type II transmembrane serine proteases: insights into an emerging class of cell surface proteolytic enzymes. J. Biol. Chem. 276, 857–860 (2001).
  CAS PubMed Google Scholar
• Velasco, G., Cal, S., Quesada, V., Sanchez, L. M. & Lopez-Otin, C. Matriptase-2, a membrane-bound mosaic serine proteinase predominantly expressed in human liver and showing degrading activity against extracellular matrix proteins. J. Biol. Chem. 277, 37637–37646 (2002).
  CAS PubMed Google Scholar
• Wex, T., Wex, H. & Bromme, D. The human cathepsin F gene — a fusion product between an ancestral cathepsin and cystatin gene. Biol. Chem. 380, 1439–1442 (1999).
  CAS PubMed Google Scholar
• Nagler, D. K., Sulea, T. & Menard, R. Full-length cDNA of human cathepsin F predicts the presence of a cystatin domain at the N-terminus of the cysteine protease zymogen. Biochem. Biophys. Res. Commun. 257, 313–318 (1999).
  CAS PubMed Google Scholar
• McQuibban, G. A. et al. Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3. Science 289, 1202–1206 (2000).
  CAS PubMed Google Scholar
• Tam, E. M., Wu, Y. I., Butler, G. S., Stack, M. S. & Overall, C. M. Collagen binding properties of the membrane type-1 matrix metalloproteinase (MT1–MMP) hemopexin C domain. The ectodomain of the 44-kDa autocatalytic product of MT1_–_MMP inhibits cell invasion by disrupting native type I collagen cleavage. J. Biol. Chem. 277, 39005–39014 (2002).
  CAS PubMed Google Scholar
• Ehlers, M. R., Fox, E. A., Strydom, D. J. & Riordan, J. F. Molecular cloning of human testicular angiotensin-converting enzyme: the testis isozyme is identical to the C-terminal half of endothelial angiotensin-converting enzyme. Proc. Natl Acad. Sci. USA 86, 7741–7745 (1989).
  CAS PubMed PubMed Central Google Scholar
• Azuma, T., Liu, W. G., Vander Laan, D. J., Bowcock, A. M. & Taggart, R. T. Human gastric cathepsin E gene. Multiple transcripts result from alternative polyadenylation of the primary transcripts of a single gene locus at 1q31–q32. J. Biol. Chem. 267, 1609–1614 (1992).
  CAS PubMed Google Scholar
• Freije, J. M. et al. Molecular cloning and expression of collagenase-3, a novel human matrix metalloproteinase produced by breast carcinomas. J. Biol. Chem. 269, 16766–16773 (1994).
  CAS PubMed Google Scholar
• Heuze-Vourc'h, N., Leblond, V. & Courty, Y. Complex alternative splicing of the hKLK3 gene coding for the tumor marker PSA (prostate-specific-antigen). Eur. J. Biochem. 270, 706–714 (2003).
  CAS PubMed Google Scholar
• Rieder, M. J., Taylor, S. L., Clark, A. G. & Nickerson, D. A. Sequence variation in the human angiotensin converting enzyme. Nature Genet. 22, 59–62 (1999).
  CAS PubMed Google Scholar
• Williams, A. G. et al. The ACE gene and muscle performance. Nature 403, 614 (2000).
  CAS PubMed Google Scholar
• Niu, T., Chen, X. & Xu, X. Angiotensin converting enzyme gene insertion/deletion polymorphism and cardiovascular disease: therapeutic implications. Drugs 62, 977–993 (2002).
  CAS PubMed Google Scholar
• Van Eerdewegh, P. et al. Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness. Nature 418, 426–430 (2002). Together with reference 74, this paper illustrates the increased susceptibility to common diseases that is associated with genetic variation in some protease genes.
  CAS PubMed Google Scholar
• Horikawa, Y. et al. Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nature Genet. 26, 163–175 (2000).
  CAS PubMed Google Scholar
• Devlin, A. M. et al. Glutamate carboxypeptidase II: a polymorphism associated with lower levels of serum folate and hyperhomocysteinemia. Hum. Mol. Genet. 9, 2837–2844 (2000).
  CAS PubMed Google Scholar
• Yamada, Y. et al. Prediction of the risk of myocardial infarction from polymorphisms in candidate genes. N. Engl. J. Med. 347, 1916–1923 (2002).
  CAS PubMed Google Scholar
• Murphy, G. et al. Matrix metalloproteinases in arthritic disease. Arthritis Res. 4 (Suppl.) 39–49 (2002).
  Google Scholar
• Yong, V. W., Power, C., Forsyth, P. & Edwards, D. R. Metalloproteinases in biology and pathology of the nervous system. Nature Rev. Neurosci. 2, 502–511 (2001).
  CAS Google Scholar
• Brinckerhoff, C. E. & Matrisian, L. M. Matrix metalloproteinases: a tail of a frog that became a prince. Nature Rev. Mol. Cell Biol. 3, 207–214 (2002).
  CAS Google Scholar
• Parks, W. C. & Shapiro, S. D. Matrix metalloproteinases in lung biology. Respir. Res. 2, 10–19 (2001).
  CAS PubMed Google Scholar
• Lomas, D. A. & Carrell, R. W. Serpinopathies and the conformational dementias. Nature Rev. Genet. 3, 759–768 (2002).
  CAS PubMed Google Scholar
• Carrell, R. W. & Lomas, D. A. α1-antitrypsin deficiency — a model for conformational diseases. N. Engl. J. Med. 346, 45–53 (2002).
  CAS PubMed Google Scholar
• Hardy, J. & Selkoe, D. J. The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science 297, 353–356 (2002).
  CAS PubMed Google Scholar
• Bowen, D. J. Haemophilia A and haemophilia B: molecular insights. Mol. Pathol. 55, 1–18 (2002).
  CAS PubMed PubMed Central Google Scholar
• Hauri, H. P., Kappeler, F., Andersson, H. & Appenzeller, C. ERGIC-53 and traffic in the secretory pathway. J. Cell. Sci. 113, 587–596 (2000).
  CAS PubMed Google Scholar
• Bignell, G. R. et al. Identification of the familial cylindromatosis tumour-suppressor gene. Nature Genet. 25, 160–165 (2000).
  CAS PubMed Google Scholar
• Wang, J. et al. Inherited human caspase 10 mutations underlie defective lymphocyte and dendritic cell apoptosis in autoimmune lymphoproliferative syndrome type II. Cell 98, 47–58 (1999).
  CAS PubMed Google Scholar
• Boatright, K. M. et al. A unified model for apical caspase activation. Mol. Cell 11, 529–541 (2003).
  CAS PubMed Google Scholar
• Huang, Y. & Wang, K. K. The calpain family and human disease. Trends Mol. Med. 7, 355–362 (2001).
  CAS PubMed Google Scholar
• Levy, G. G. et al. Mutations in a member of the ADAMTS gene family cause thrombotic thrombocytopenic purpura. Nature 413, 488–494 (2001).
  CAS PubMed Google Scholar
• Guipponi, M. et al. The transmembrane serine protease (TMPRSS3) mutated in deafness DFNB8/10 activates the epithelial sodium channel (ENaC) in vitro. Hum. Mol. Genet. 11, 2829–2836 (2002).
  CAS PubMed Google Scholar
• Citron, M. et al. Mutant presenilins of Alzheimer's disease increase production of 42-residue amyloid β-protein in both transfected cells and transgenic mice. Nature Med. 3, 67–72 (1997).
  CAS PubMed Google Scholar
• Gehring, N. H. et al. Increased efficiency of mRNA 3′ end formation: a new genetic mechanism contributing to hereditary thrombophilia. Nature Genet. 28, 389–392 (2001).
  CAS PubMed Google Scholar
• De Jonghe, C. et al. Aberrant splicing in the presenilin-1 intron 4 mutation causes presenile Alzheimer's disease by increased Aβ42 secretion. Hum. Mol. Genet. 8, 1529–1540 (1999).
  CAS PubMed Google Scholar
• Molinari, F. et al. Truncating neurotrypsin mutation in autosomal recessive nonsyndromic mental retardation. Science 298, 1779–1781 (2002).
  CAS PubMed Google Scholar
• Casari, G. et al. Spastic paraplegia and OXPHOS impairment caused by mutations in paraplegin, a nuclear-encoded mitochondrial metalloprotease. Cell 93, 973–983 (1998).
  CAS PubMed Google Scholar
• Chun, H. J. et al. Pleiotropic defects in lymphocyte activation caused by caspase-8 mutations lead to human immunodeficiency. Nature 419, 395–399 (2002).
  CAS PubMed Google Scholar
• Belaaouaj, A. et al. Mice lacking neutrophil elastase reveal impaired host defense against Gram negative bacterial sepsis. Nature Med. 4, 615–618 (1998).
  CAS PubMed Google Scholar
• Horwitz, M., Benson, K. F., Person, R. E., Aprikyan, A. G. & Dale, D. C. Mutations in ELA2, encoding neutrophil elastase, define a 21-day biological clock in cyclic haematopoiesis. Nature Genet. 23, 433–436 (1999).
  CAS PubMed Google Scholar
• Pendás, A. M. et al. Defective prelamin A processing and muscular and adipocyte alterations in Zmpste24 metalloproteinase-deficient mice. Nature Genet. 31, 94–99 (2002). Together with references 101 and 102, this paper is an example of the usefulness of mouse models and genetic approaches to identify the in vivo substrates of proteases.
  PubMed Google Scholar
• Li, Q., Park, P. W., Wilson, C. L. & Parks, W. C. Matrilysin shedding of syndecan-1 regulates chemokine mobilization and transepithelial efflux of neutrophils in acute lung injury. Cell 111, 635–646 (2002).
  CAS PubMed Google Scholar
• Wilson, C. L. et al. Regulation of intestinal α-defensin activation by the metalloproteinase matrilysin in innate host defense. Science 286, 113–117 (1999).
  CAS PubMed Google Scholar
• Ranger, A. M., Malynn, B. A. & Korsmeyer, S. J. Mouse models of cell death. Nature Genet. 28, 113–118 (2001).
  CAS PubMed Google Scholar
• Rakic, J. M. et al. Role of plasminogen activator-plasmin system in tumor angiogenesis. Cell Mol. Life Sci. 60, 463–473 (2003).
  CAS PubMed Google Scholar
• Lund, L. R. et al. Functional overlap between two classes of matrix-degrading proteases in wound healing. EMBO J. 18, 4645–4656 (1999).
  CAS PubMed PubMed Central Google Scholar
• Blasi, F. & Carmeliet, P. uPAR: a versatile signalling orchestrator. Nature Rev. Mol. Cell Biol. 3, 932–943 (2002).
  CAS Google Scholar
• Holmbeck, K. et al. MT1–MMP-deficient mice develop dwarfism, osteopenia, arthritis, and connective tissue disease due to inadequate collagen turnover. Cell 99, 81–92 (1999).
  CAS PubMed Google Scholar
• Zhou, Z. et al. Impaired endochondral ossification and angiogenesis in mice deficient in membrane-type matrix metalloproteinase I. Proc. Natl Acad. Sci. USA 97, 4052–4057 (2000).
  CAS PubMed PubMed Central Google Scholar
• Caterina, J. J. et al. Enamelysin (matrix metalloproteinase 20)-deficient mice display an amelogenesis imperfecta phenotype. J. Biol. Chem. 277, 49598–49604 (2002).
  CAS PubMed Google Scholar
• Coussens, L. M., Shapiro, S. D., Soloway, P. D. & Werb, Z. Models for gain-of-function and loss-of-function of MMPs: transgenic and gene targeted mice. Methods Mol. Biol. 151, 149–179 (2001).
  CAS PubMed Google Scholar
• Wilson, S. M. et al. Synaptic defects in ataxia mice result from a mutation in Usp14, encoding a ubiquitin-specific protease. Nature Genet. 32, 420–425 (2002). An interesting example of a mouse disease that is caused by a mutation in a protease gene, the human orthologue of which has not yet been linked to an equivalent disorder.
  CAS PubMed Google Scholar
• Neuhold, L. A. et al. Postnatal expression in hyaline cartilage of constitutively active human collagenase-3 (MMP-13) induces osteoarthritis in mice. J. Clin. Invest. 107, 35–44 (2001).
  CAS PubMed PubMed Central Google Scholar
• Yu, Y. & Bradley, A. Engineering chromosomal rearrangements in mice. Nature Rev. Genet. 2, 780–790 (2001).
  CAS PubMed Google Scholar
• Stanford, W. L., Cohn, J. B. & Cordes, S. P. Gene-trap mutagenesis: past, present and beyond. Nature Rev. Genet. 2, 756–768 (2001).
  CAS PubMed Google Scholar
• Southan, C. A genomic perspective on human proteases as drug targets. Drug Discov. Today 6, 681–688 (2001). A discussion of the relevance of proteases as therapeutic targets.
  CAS PubMed Google Scholar
• Overall, C. M. & López-Otín, C. Strategies for MMP inhibition in cancer: innovations for the post-trial era. Nature Rev. Cancer 2, 657–672 (2002).
  CAS Google Scholar
• Soto, C. Protein misfolding and disease; protein refolding and therapy. FEBS Lett. 498, 204–207 (2001).
  CAS PubMed Google Scholar
• Crowther, D. C. Familial conformational diseases and dementias. Hum. Mutat. 20, 1–14 (2002).
  CAS PubMed Google Scholar
• Cushman, D. W. & Ondetti, M. A. Design of angiotensin converting enzyme inhibitors. Nature Med. 5, 1110–1113 (1999). Together with reference 120, this article represents an example of the successful introduction of protease inhibitors to treat human disease.
  CAS PubMed Google Scholar
• Menendez-Arias, L. Targeting HIV: antiretroviral therapy and development of drug resistance. Trends Pharmacol. Sci. 23, 381–388 (2002).
  CAS PubMed Google Scholar
• Coussens, L. M., Fingleton, B. & Matrisian, L. M. Matrix metalloproteinase inhibitors and cancer: trials and tribulations. Science 295, 2387–2392 (2002). An excellent analysis of the lack of success of most MMP inhibitors developed for treating cancer and discussion of alternatives for future improvement in this field.
  CAS PubMed Google Scholar
• Gomis-Ruth, F. X. et al. Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1. Nature 389, 77–81 (1997).
  CAS PubMed Google Scholar
• Bode, W. & Huber, R. Structural basis of the endoproteinase-protein inhibitor interaction. Biochim. Biophys. Acta 1477, 241–252 (2000).
  CAS PubMed Google Scholar
• Vendrell, J., Querol, E. & Aviles, F. X. Metallocarboxypeptidases and their protein inhibitors: structure, function and biomedical properties. Biochim. Biophys. Acta 1477, 284–298 (2000).
  CAS PubMed Google Scholar
• Morgunova, E., Tuuttila, A., Bergmann, U. & Tryggvason, K. Structural insight into the complex formation of latent matrix metalloproteinase 2 with tissue inhibitor of metalloproteinase 2. Proc. Natl Acad. Sci. USA 99, 7414–7419 (2002).
  CAS PubMed PubMed Central Google Scholar
• Turk, V., Turk, B. & Turk, D. Lysosomal cysteine proteases: facts and opportunities. EMBO J. 20, 4629–4633 (2001).
  CAS PubMed PubMed Central Google Scholar
• Anel, R. L. & Kumar, A. Experimental and emerging therapies for sepsis and septic shock. Expert Opin. Investig. Drugs 10, 1471–1485 (2001).
  CAS PubMed Google Scholar
• Desnick, R. J. & Schuchman, E. H. Enzyme replacement and enhancement therapies: lessons from lysosomal disorders. Nature Rev. Genet. 3, 954–966 (2002). A comprehensive review that discusses the successes and shortcomings of present strategies to treat inherited metabolic disorders.
  CAS PubMed Google Scholar
• Roth, D. A. et al. Human recombinant factor IX: safety and efficacy studies in hemophilia B patients previously treated with plasma-derived factor IX concentrates. Blood 98, 3600–3606 (2001).
  CAS PubMed Google Scholar
• Selkoe, D. J. Deciphering the genesis and fate of amyloid β-protein yields novel therapies for Alzheimer disease. J. Clin. Invest. 110, 1375–1381 (2002).
  CAS PubMed PubMed Central Google Scholar
• Kay, M. A. et al. Evidence for gene transfer and expression of factor IX in haemophilia B patients treated with an AAV vector. Nature Genet. 24, 257–261 (2000).
  CAS PubMed Google Scholar
• Olson, M. V. & Varki, A. Sequencing the chimpanzee genome: insights into human evolution and disease. Nature Rev. Genet. 4, 20–28 (2003). An excellent analysis of the relevance of comparative genomics and discussion of the argument that gene loss might be an important mechanism of rapid evolutionary change.
  CAS PubMed Google Scholar
• Kheradmand, F. & Werb, Z. Shedding light on sheddases: role in growth and development. Bioessays 24, 8–12 (2002). Together with reference 134, this review describes the functional relevance of the protease-mediated process of ectodomain shedding of membrane proteins.
  CAS PubMed Google Scholar
• Arribas, J. & Borroto, A. Protein ectodomain shedding. Chem. Rev. 102, 4627–4638 (2002).
  CAS PubMed Google Scholar
• Rudner, D. Z., Fawcett, P. & Losick, R. A family of membrane-embedded metalloproteases involved in regulated proteolysis of membrane-associated transcription factors. Proc. Natl Acad. Sci. USA 96, 14765–14770 (1999).
  CAS PubMed PubMed Central Google Scholar
• Hoppe, T., Rape, M. & Jentsch, S. Membrane-bound transcription factors: regulated release by RIP or RUP. Curr. Opin. Cell Biol. 13, 344–348 (2001).
  CAS PubMed Google Scholar
• Brown, M. S., Ye, J., Rawson, R. B. & Goldstein, J. L. Regulated intramembrane proteolysis: a control mechanism conserved from bacteria to humans. Cell 100, 391–398 (2000). An excellent analysis of the fascinating process that involves the participation of proteases that hydrolyze their substrates in the hydrophobic environment of the lipid bilayers.
  CAS PubMed Google Scholar
• Hopkins, A. L. & Groom, C. R. The druggable genome. Nature Rev. Drug Discov. 1, 727–730 (2002).
  CAS Google Scholar
• McLysaght, A., Hokamp, K. & Wolfe, K. H. Extensive genomic duplication during early chordate evolution. Nature Genet. 31, 200–204 (2002).
  CAS PubMed Google Scholar
• Samonte, R. V. & Eichler, E. E. Segmental duplications and the evolution of the primate genome. Nature Rev. Genet. 3, 65–72 (2002).
  CAS PubMed Google Scholar
• Ross, J., Jiang, H., Kanost, M. R. & Wang, Y. Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships. Gene 304, 117–131 (2003).
  CAS PubMed Google Scholar
• Lespinet, O., Wolf, Y. I., Koonin, E. V. & Aravind, L. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12, 1048–1059 (2002).
  CAS PubMed PubMed Central Google Scholar
• Nardi, J. B., Martos, R., Walden, K. K., Lampe, D. J. & Robertson, H. M. Expression of lacunin, a large multidomain extracellular matrix protein, accompanies morphogenesis of epithelial monolayers in Manduca sexta. Insect Biochem. Mol. Biol. 29, 883–897 (1999).
  CAS PubMed Google Scholar